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calibre should be saving a metadata.calibre file to the root of the device, in order to cache the scanned data. THe first time you connect, it may take a while, but afterwards calibre will finish scanning in a matter of seconds.
Is that file getting deleted somehow? Or are you changing most of the books around in some other manner than using calibre, causing calibre to need to scan tons more books that have not been added to the cache yet?
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